User: meerapprasad

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meerapprasad10
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Posts by meerapprasad

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Comment: C: Samtools view error when converting sam to bam file using sc-ATAC-seq data from
... 1300:@RG ID:A2.08,P2.14,A1.04,P1.05 SM:Barcode05838 4099:@PG ID:bowtie2-E6859AC-EAA2107 PN:bowtie2 VN:2.2.5 CL:"/mnt/users/sai/miniconda2/bin/bowtie2-align-s --wrapper basic-0 -X2000 -p 18 --rg-id kidney_marrow_KO_gata2B -x /mnt/users/sai/Script/genomes/bowtie2/GRCz10/GRCz10 -1 /mnt/AlignedData/181 ...
written 29 days ago by meerapprasad10
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Comment: C: Samtools view error when converting sam to bam file using sc-ATAC-seq data from
... Hi! Thank you so much for the reply! I tried what you had suggested but got the same error: [W::sam_read1] Parse error at line 1 [main_samview] truncated file. Do you have any other recommendations? ...
written 29 days ago by meerapprasad10
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Comment: C: Samtools view error when converting sam to bam file using sc-ATAC-seq data from
... Hi John, Thank you so much for the reply! I am new to samtools so I am not sure what the numbers before the @RG are, but I tried what you had suggested and got this error: [E::sam_parse1] missing SAM header [W::sam_read1] Parse error at line 191 [main_samview] truncated file. What do you recomm ...
written 29 days ago by meerapprasad10
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Samtools view error when converting sam to bam file using sc-ATAC-seq data from Cell Ranger pipeline
... Hi! I am working on a single cell ATAC sequencing project and am having an issue using samtools to split a bam file based on my wild-type and knock-out. The data came from 10X sequencing and they used the Cell Ranger pipeline for analysis. One analysis that the Cell Ranger conducted was t-sne which ...
samtools view samtools cell ranger sc-atac-seq written 29 days ago by meerapprasad10 • updated 29 days ago by John Marshall1.7k
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Comment: C: "bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out h
... Hi Gautier, Thank you! I have been in contact with our HPC - expert and he has helped me up the RAM as much as possible. Unfortunately, it still has not been working. Would you recommend another alignment such as BWA? ...
written 7 months ago by meerapprasad10
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Comment: C: "bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out h
... Hello! Yes, I think we have been running out of memory. Are you familiar with any other ways to map our sequences to this database? ...
written 7 months ago by meerapprasad10
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"bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out how to fix my script
... Hello! I am working on assembling a transcriptome of the terminal ganglion of the cricket (Gryllus bimaculatus). We are working on a non-model species and thus did not remove ribosomal contamination during library prep. We want to remove ribosomal contamination bioinformatically, and I am mapping ou ...
software error assembly alignment bowtie2 written 7 months ago by meerapprasad10 • updated 5 months ago by Biostar ♦♦ 20

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